Keyboard Shortcuts
In pyMolDyn, several keyboard shortcuts are available. Note, on Linux machines, use "Ctrl" (Control) instead of "Cmd" (Command).
| Shortcut | Action |
|---|---|
| Alt+1 | Open Most Recent File |
| Cmd+1 | Export Bonds |
| Cmd+2 | Export Bond angles |
| Cmd+3 | Export Bond dihedral angles |
| Cmd+4 | Export Cavity Information (domains) |
| Cmd+5 | Export Cavity Information (surface method) |
| Cmd+6 | Export Cavity Information (center method) |
| Cmd+I | Open Settings |
| Cmd+O | Open Files for calculation |
| d | Show Domains |
| c | Show cavities (surface method) |
| f | Show cavities (center method) |
| r | Reset camera |
| arrow Keys | Rotate camera |
Cell Shape Description
pyMolDyn supports cell shapes corresponding to all seven 3D Bravais lattice systems. The cell shape and size are set using the Bravais lattice parameters as shown below, with angles given in radians. The application reads these settings from the second line of the .xyz file and uses them for all frames.
The following snippet shows the second line for a hexgonal cell:
HEX 17.68943 22.61158
Additional comments on this line will be ignored.
Full resolution images of cell shape information: TRI, MON, ORT, TET, RHO, CUB, HEX
Pair Distribution Function Smoothing Kernels
The PDF plotting widget in pyMolDyn uses one of seven selectable smoothing kernels to create a graph. The kernels, their formulas with a bandwidth σ and their plots for σ=1, are given here. Please note that for a bandwidth of 0, the data is not smoothened, but individual peaks of height 1 are rendered. This can be useful, but visually overlapping peaks might be misleading.